Starting phenix.real_space_refine on Sat Dec 28 14:58:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ezh_31387/12_2024/7ezh_31387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezh_31387/12_2024/7ezh_31387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ezh_31387/12_2024/7ezh_31387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezh_31387/12_2024/7ezh_31387.map" model { file = "/net/cci-nas-00/data/ceres_data/7ezh_31387/12_2024/7ezh_31387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezh_31387/12_2024/7ezh_31387.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 5643 2.51 5 N 1489 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2306 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.19, per 1000 atoms: 0.59 Number of scatterers: 8838 At special positions: 0 Unit cell: (106.59, 112.86, 119.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1634 8.00 N 1489 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 41.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.509A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.995A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.053A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.928A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.513A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 removed outlier: 5.355A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.657A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 69 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 74 through 105 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 110 through 145 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.589A pdb=" N ARG D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 173 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 202 through 218 Processing helix chain 'D' and resid 218 through 245 removed outlier: 3.693A pdb=" N GLY D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 339 removed outlier: 3.508A pdb=" N LYS D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 349 through 370 removed outlier: 3.719A pdb=" N SER D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 384 removed outlier: 4.364A pdb=" N MET D 382 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.662A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.658A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.926A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.483A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.722A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.771A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.801A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 180 through 187 removed outlier: 3.609A pdb=" N ARG D 197 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.730A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.760A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2822 1.35 - 1.47: 2251 1.47 - 1.59: 3841 1.59 - 1.71: 1 1.71 - 1.83: 107 Bond restraints: 9022 Sorted by residual: bond pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.462 1.635 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.537 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" N VAL H 119 " pdb=" CA VAL H 119 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.15e-02 7.56e+03 1.42e+01 bond pdb=" N SER H 120 " pdb=" CA SER H 120 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.13e+00 bond pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.46e+00 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11975 1.93 - 3.85: 225 3.85 - 5.78: 26 5.78 - 7.71: 9 7.71 - 9.63: 3 Bond angle restraints: 12238 Sorted by residual: angle pdb=" N SER A 326 " pdb=" CA SER A 326 " pdb=" C SER A 326 " ideal model delta sigma weight residual 111.14 104.94 6.20 1.08e+00 8.57e-01 3.30e+01 angle pdb=" C GLN D 153 " pdb=" CA GLN D 153 " pdb=" CB GLN D 153 " ideal model delta sigma weight residual 111.88 104.45 7.43 1.41e+00 5.03e-01 2.77e+01 angle pdb=" C THR A 329 " pdb=" CA THR A 329 " pdb=" CB THR A 329 " ideal model delta sigma weight residual 110.42 118.59 -8.17 1.99e+00 2.53e-01 1.69e+01 angle pdb=" CA ALA H 136 " pdb=" C ALA H 136 " pdb=" O ALA H 136 " ideal model delta sigma weight residual 121.54 117.25 4.29 1.16e+00 7.43e-01 1.37e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 121.71 -8.53 2.37e+00 1.78e-01 1.30e+01 ... (remaining 12233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4876 16.62 - 33.23: 384 33.23 - 49.85: 55 49.85 - 66.46: 13 66.46 - 83.08: 8 Dihedral angle restraints: 5336 sinusoidal: 2000 harmonic: 3336 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 149.62 -56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CA LEU D 200 " pdb=" C LEU D 200 " pdb=" N PRO D 201 " pdb=" CA PRO D 201 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 5333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1296 0.079 - 0.159: 110 0.159 - 0.238: 3 0.238 - 0.317: 0 0.317 - 0.397: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA THR A 329 " pdb=" N THR A 329 " pdb=" C THR A 329 " pdb=" CB THR A 329 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA GLN D 153 " pdb=" N GLN D 153 " pdb=" C GLN D 153 " pdb=" CB GLN D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA THR A 327 " pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CB THR A 327 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 1407 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 214 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU D 214 " 0.074 2.00e-02 2.50e+03 pdb=" O LEU D 214 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU D 215 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 325 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C CYS A 325 " 0.072 2.00e-02 2.50e+03 pdb=" O CYS A 325 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 326 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.007 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR B 105 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.032 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2178 2.80 - 3.33: 8692 3.33 - 3.85: 14958 3.85 - 4.38: 17905 4.38 - 4.90: 30344 Nonbonded interactions: 74077 Sorted by model distance: nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASN D 304 " pdb=" NZ LYS D 308 " model vdw 2.283 3.120 nonbonded pdb=" O ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 3.040 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.360 3.040 ... (remaining 74072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 9022 Z= 0.276 Angle : 0.680 9.633 12238 Z= 0.411 Chirality : 0.045 0.397 1410 Planarity : 0.007 0.057 1537 Dihedral : 12.747 83.080 3172 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 0.74 % Allowed : 2.33 % Favored : 96.93 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1127 helix: -1.09 (0.22), residues: 406 sheet: -0.18 (0.30), residues: 277 loop : -1.01 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.022 0.002 PHE D 354 TYR 0.037 0.005 TYR B 105 ARG 0.053 0.008 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 317 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7518 (ttpt) REVERT: A 33 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6426 (mt-10) REVERT: A 186 GLU cc_start: 0.6591 (tt0) cc_final: 0.5926 (tt0) REVERT: A 197 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7524 (mtpp) REVERT: A 210 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7453 (mmtt) REVERT: A 243 MET cc_start: 0.7404 (tpp) cc_final: 0.7156 (tpp) REVERT: A 272 ASP cc_start: 0.7260 (t0) cc_final: 0.6936 (t0) REVERT: A 330 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6424 (mmtt) REVERT: B 43 ILE cc_start: 0.8993 (mm) cc_final: 0.8747 (mt) REVERT: B 83 ASP cc_start: 0.6948 (t0) cc_final: 0.6418 (t0) REVERT: B 121 CYS cc_start: 0.6087 (t) cc_final: 0.5699 (t) REVERT: B 188 MET cc_start: 0.7480 (mmm) cc_final: 0.7132 (mmm) REVERT: B 204 CYS cc_start: 0.7584 (m) cc_final: 0.7309 (m) REVERT: B 205 ASP cc_start: 0.7097 (p0) cc_final: 0.6852 (p0) REVERT: B 219 ARG cc_start: 0.6994 (mmt180) cc_final: 0.6775 (mmt-90) REVERT: B 228 ASP cc_start: 0.5841 (t0) cc_final: 0.5626 (t70) REVERT: B 232 ILE cc_start: 0.8525 (tt) cc_final: 0.8196 (tt) REVERT: B 239 ASN cc_start: 0.7401 (m-40) cc_final: 0.7189 (m-40) REVERT: B 261 LEU cc_start: 0.8006 (mp) cc_final: 0.7803 (mt) REVERT: B 277 SER cc_start: 0.8371 (t) cc_final: 0.7748 (m) REVERT: B 312 ASP cc_start: 0.5952 (t0) cc_final: 0.5590 (t70) REVERT: B 322 ASP cc_start: 0.6255 (t0) cc_final: 0.6038 (t0) REVERT: B 333 ASP cc_start: 0.6065 (m-30) cc_final: 0.5609 (m-30) REVERT: D 47 LEU cc_start: 0.7675 (mt) cc_final: 0.7423 (mt) REVERT: D 178 ILE cc_start: 0.7526 (mt) cc_final: 0.7284 (mt) REVERT: D 218 PHE cc_start: 0.7195 (t80) cc_final: 0.6946 (t80) REVERT: D 314 MET cc_start: 0.7046 (tpp) cc_final: 0.6522 (mpp) REVERT: H 94 TYR cc_start: 0.7747 (m-80) cc_final: 0.7327 (m-80) REVERT: H 140 MET cc_start: 0.8153 (mmm) cc_final: 0.7888 (mmm) REVERT: H 173 TYR cc_start: 0.8330 (m-80) cc_final: 0.8067 (m-80) REVERT: H 178 LEU cc_start: 0.8174 (tp) cc_final: 0.7957 (tt) REVERT: H 226 VAL cc_start: 0.7971 (t) cc_final: 0.7670 (m) REVERT: H 243 THR cc_start: 0.8580 (m) cc_final: 0.8336 (p) outliers start: 7 outliers final: 2 residues processed: 322 average time/residue: 0.2224 time to fit residues: 97.0029 Evaluate side-chains 276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 326 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.0570 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 153 GLN H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9022 Z= 0.184 Angle : 0.574 7.275 12238 Z= 0.306 Chirality : 0.042 0.140 1410 Planarity : 0.004 0.043 1537 Dihedral : 5.531 28.817 1236 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.22 % Allowed : 11.23 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1127 helix: 1.02 (0.26), residues: 412 sheet: -0.14 (0.29), residues: 280 loop : -0.46 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS G 44 PHE 0.020 0.002 PHE D 218 TYR 0.012 0.001 TYR D 370 ARG 0.005 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7459 (ttpt) cc_final: 0.7037 (ttpt) REVERT: A 210 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7249 (mmtt) REVERT: A 261 ASP cc_start: 0.7187 (t0) cc_final: 0.6933 (t0) REVERT: A 272 ASP cc_start: 0.7218 (t0) cc_final: 0.6871 (t0) REVERT: A 330 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6603 (mmtt) REVERT: B 74 SER cc_start: 0.8159 (m) cc_final: 0.7955 (t) REVERT: B 135 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7744 (m) REVERT: B 137 ARG cc_start: 0.7567 (mmt-90) cc_final: 0.7305 (mmt180) REVERT: B 155 ASN cc_start: 0.7649 (t0) cc_final: 0.7441 (t0) REVERT: B 188 MET cc_start: 0.7622 (mmm) cc_final: 0.7234 (mmm) REVERT: B 205 ASP cc_start: 0.7203 (p0) cc_final: 0.6842 (p0) REVERT: B 219 ARG cc_start: 0.7069 (mmt180) cc_final: 0.6852 (mmt90) REVERT: B 232 ILE cc_start: 0.8487 (tt) cc_final: 0.8180 (tt) REVERT: B 256 ARG cc_start: 0.7970 (mpp80) cc_final: 0.7292 (mtt90) REVERT: B 261 LEU cc_start: 0.8167 (mp) cc_final: 0.7962 (mp) REVERT: B 275 SER cc_start: 0.8114 (t) cc_final: 0.7851 (m) REVERT: B 277 SER cc_start: 0.8377 (t) cc_final: 0.7822 (m) REVERT: B 312 ASP cc_start: 0.5826 (t0) cc_final: 0.5446 (t70) REVERT: B 331 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 333 ASP cc_start: 0.6304 (m-30) cc_final: 0.5696 (m-30) REVERT: D 218 PHE cc_start: 0.7326 (t80) cc_final: 0.6929 (t80) REVERT: D 323 PHE cc_start: 0.7836 (m-10) cc_final: 0.7580 (m-80) REVERT: H 95 TYR cc_start: 0.7843 (m-10) cc_final: 0.7623 (m-10) REVERT: H 178 LEU cc_start: 0.8125 (tp) cc_final: 0.7870 (tt) REVERT: H 243 THR cc_start: 0.8542 (m) cc_final: 0.8264 (p) outliers start: 21 outliers final: 11 residues processed: 287 average time/residue: 0.2033 time to fit residues: 79.7096 Evaluate side-chains 285 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9022 Z= 0.252 Angle : 0.576 7.110 12238 Z= 0.305 Chirality : 0.043 0.138 1410 Planarity : 0.004 0.050 1537 Dihedral : 5.207 27.384 1235 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.07 % Allowed : 14.83 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1127 helix: 1.44 (0.26), residues: 406 sheet: -0.15 (0.30), residues: 289 loop : -0.20 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.008 0.001 HIS B 142 PHE 0.016 0.002 PHE D 218 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7308 (mt) cc_final: 0.7043 (mp) REVERT: A 29 LYS cc_start: 0.7332 (ttpt) cc_final: 0.6871 (ttpt) REVERT: A 33 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6413 (mt-10) REVERT: A 210 LYS cc_start: 0.7590 (mmmt) cc_final: 0.7350 (mmtt) REVERT: A 261 ASP cc_start: 0.7118 (t0) cc_final: 0.6853 (t0) REVERT: A 272 ASP cc_start: 0.7157 (t0) cc_final: 0.6831 (t0) REVERT: A 330 LYS cc_start: 0.7227 (mmtt) cc_final: 0.6718 (mmtt) REVERT: B 68 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7420 (tpp80) REVERT: B 129 ARG cc_start: 0.6531 (mmp80) cc_final: 0.6292 (mmp80) REVERT: B 135 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7918 (m) REVERT: B 137 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7315 (mmt180) REVERT: B 168 LEU cc_start: 0.7676 (tp) cc_final: 0.7220 (tt) REVERT: B 188 MET cc_start: 0.7479 (mmm) cc_final: 0.7049 (mmm) REVERT: B 205 ASP cc_start: 0.7081 (p0) cc_final: 0.6638 (p0) REVERT: B 219 ARG cc_start: 0.7198 (mmt180) cc_final: 0.6889 (mmt90) REVERT: B 230 ASN cc_start: 0.7573 (m-40) cc_final: 0.7213 (m110) REVERT: B 239 ASN cc_start: 0.7448 (m-40) cc_final: 0.7052 (m-40) REVERT: B 256 ARG cc_start: 0.7978 (mpp80) cc_final: 0.7407 (mtt180) REVERT: B 258 ASP cc_start: 0.7570 (t70) cc_final: 0.7176 (t0) REVERT: B 263 THR cc_start: 0.8288 (m) cc_final: 0.8074 (p) REVERT: B 275 SER cc_start: 0.8115 (t) cc_final: 0.7855 (m) REVERT: B 277 SER cc_start: 0.8265 (t) cc_final: 0.7707 (m) REVERT: B 301 LYS cc_start: 0.8235 (mmmt) cc_final: 0.8002 (mtpp) REVERT: B 312 ASP cc_start: 0.5976 (t0) cc_final: 0.5698 (t70) REVERT: B 331 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7671 (p) REVERT: B 333 ASP cc_start: 0.6159 (m-30) cc_final: 0.5646 (m-30) REVERT: D 98 ASN cc_start: 0.8350 (m110) cc_final: 0.8109 (m-40) REVERT: D 154 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8135 (p) REVERT: H 60 TYR cc_start: 0.8075 (m-80) cc_final: 0.7720 (m-80) REVERT: H 87 ARG cc_start: 0.7144 (ptm160) cc_final: 0.6804 (ptm160) REVERT: H 94 TYR cc_start: 0.8041 (m-80) cc_final: 0.7736 (m-80) REVERT: H 95 TYR cc_start: 0.7957 (m-10) cc_final: 0.7707 (m-10) REVERT: H 173 TYR cc_start: 0.8491 (m-80) cc_final: 0.8169 (m-80) REVERT: H 178 LEU cc_start: 0.8194 (tp) cc_final: 0.7947 (tt) REVERT: H 243 THR cc_start: 0.8637 (m) cc_final: 0.8218 (p) outliers start: 29 outliers final: 19 residues processed: 287 average time/residue: 0.2205 time to fit residues: 85.9639 Evaluate side-chains 288 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9022 Z= 0.276 Angle : 0.582 6.976 12238 Z= 0.305 Chirality : 0.043 0.142 1410 Planarity : 0.004 0.051 1537 Dihedral : 5.061 26.297 1235 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.60 % Allowed : 16.74 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1127 helix: 1.49 (0.25), residues: 413 sheet: -0.28 (0.29), residues: 301 loop : -0.16 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.002 PHE D 198 TYR 0.025 0.002 TYR D 179 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 1.035 Fit side-chains REVERT: A 29 LYS cc_start: 0.7230 (ttpt) cc_final: 0.6841 (ttpt) REVERT: A 33 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6434 (mt-10) REVERT: A 197 LYS cc_start: 0.7997 (mtpp) cc_final: 0.7779 (mtpp) REVERT: A 199 PHE cc_start: 0.7928 (m-80) cc_final: 0.7313 (m-80) REVERT: A 210 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7407 (mmtt) REVERT: A 251 ASP cc_start: 0.7215 (t0) cc_final: 0.6981 (t0) REVERT: A 261 ASP cc_start: 0.7088 (t0) cc_final: 0.6825 (t0) REVERT: A 272 ASP cc_start: 0.7126 (t0) cc_final: 0.6806 (t0) REVERT: A 330 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6756 (mmtt) REVERT: B 68 ARG cc_start: 0.7889 (ttt-90) cc_final: 0.7495 (tpp80) REVERT: B 129 ARG cc_start: 0.6560 (mmp80) cc_final: 0.6277 (mmp80) REVERT: B 135 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8244 (m) REVERT: B 137 ARG cc_start: 0.7564 (mmt-90) cc_final: 0.7343 (mmt180) REVERT: B 205 ASP cc_start: 0.7068 (p0) cc_final: 0.6603 (p0) REVERT: B 219 ARG cc_start: 0.7305 (mmt180) cc_final: 0.6995 (mmt90) REVERT: B 232 ILE cc_start: 0.8494 (tt) cc_final: 0.8161 (tt) REVERT: B 239 ASN cc_start: 0.7472 (m-40) cc_final: 0.7110 (m-40) REVERT: B 258 ASP cc_start: 0.7519 (t0) cc_final: 0.7013 (t0) REVERT: B 275 SER cc_start: 0.8155 (t) cc_final: 0.7860 (m) REVERT: B 277 SER cc_start: 0.8060 (t) cc_final: 0.7524 (m) REVERT: B 301 LYS cc_start: 0.8228 (mmmt) cc_final: 0.8020 (mtpp) REVERT: B 312 ASP cc_start: 0.6069 (t0) cc_final: 0.5824 (t70) REVERT: B 331 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7744 (p) REVERT: B 333 ASP cc_start: 0.6201 (m-30) cc_final: 0.5761 (m-30) REVERT: D 98 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8111 (m-40) REVERT: D 102 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7754 (t0) REVERT: D 154 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (p) REVERT: D 323 PHE cc_start: 0.7957 (m-10) cc_final: 0.7740 (m-80) REVERT: H 60 TYR cc_start: 0.8063 (m-80) cc_final: 0.7752 (m-80) REVERT: H 172 THR cc_start: 0.8325 (m) cc_final: 0.7998 (p) REVERT: H 243 THR cc_start: 0.8677 (m) cc_final: 0.8215 (p) outliers start: 34 outliers final: 21 residues processed: 286 average time/residue: 0.2185 time to fit residues: 84.9190 Evaluate side-chains 287 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 213 HIS B 88 ASN B 295 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9022 Z= 0.239 Angle : 0.570 7.992 12238 Z= 0.297 Chirality : 0.043 0.157 1410 Planarity : 0.004 0.049 1537 Dihedral : 4.957 25.322 1235 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.50 % Allowed : 18.01 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1127 helix: 1.66 (0.26), residues: 408 sheet: -0.28 (0.29), residues: 290 loop : -0.24 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 111 HIS 0.004 0.001 HIS A 213 PHE 0.021 0.002 PHE H 68 TYR 0.026 0.002 TYR D 179 ARG 0.004 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.915 Fit side-chains REVERT: A 29 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6813 (ttpt) REVERT: A 33 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6425 (mt-10) REVERT: A 197 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7795 (mtpp) REVERT: A 251 ASP cc_start: 0.7255 (t0) cc_final: 0.6994 (t0) REVERT: A 261 ASP cc_start: 0.7070 (t0) cc_final: 0.6794 (t0) REVERT: A 309 ASP cc_start: 0.6478 (m-30) cc_final: 0.6087 (m-30) REVERT: A 330 LYS cc_start: 0.7283 (mmtt) cc_final: 0.6796 (mmtt) REVERT: B 52 ARG cc_start: 0.6822 (mtp85) cc_final: 0.6603 (mtt-85) REVERT: B 68 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7555 (ttt-90) REVERT: B 101 MET cc_start: 0.8058 (ptm) cc_final: 0.7838 (ptp) REVERT: B 129 ARG cc_start: 0.6551 (mmp80) cc_final: 0.6266 (mmp80) REVERT: B 135 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8148 (m) REVERT: B 168 LEU cc_start: 0.7701 (tp) cc_final: 0.7301 (tp) REVERT: B 205 ASP cc_start: 0.7028 (p0) cc_final: 0.6624 (p0) REVERT: B 219 ARG cc_start: 0.7419 (mmt180) cc_final: 0.7128 (mmt90) REVERT: B 230 ASN cc_start: 0.7520 (m-40) cc_final: 0.7185 (m110) REVERT: B 232 ILE cc_start: 0.8485 (tt) cc_final: 0.8135 (tt) REVERT: B 239 ASN cc_start: 0.7459 (m-40) cc_final: 0.7133 (m-40) REVERT: B 254 ASP cc_start: 0.6868 (t70) cc_final: 0.6565 (t70) REVERT: B 255 LEU cc_start: 0.7867 (mp) cc_final: 0.7634 (mt) REVERT: B 258 ASP cc_start: 0.7487 (t0) cc_final: 0.7003 (t0) REVERT: B 275 SER cc_start: 0.8135 (t) cc_final: 0.7908 (t) REVERT: B 277 SER cc_start: 0.8160 (t) cc_final: 0.7609 (m) REVERT: B 298 ASP cc_start: 0.7215 (t70) cc_final: 0.6847 (t70) REVERT: B 312 ASP cc_start: 0.6074 (t0) cc_final: 0.5838 (t70) REVERT: B 331 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7878 (p) REVERT: B 333 ASP cc_start: 0.6208 (m-30) cc_final: 0.5877 (m-30) REVERT: D 98 ASN cc_start: 0.8323 (m110) cc_final: 0.8024 (m-40) REVERT: D 102 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7818 (t0) REVERT: D 154 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8152 (p) REVERT: H 60 TYR cc_start: 0.8003 (m-80) cc_final: 0.7680 (m-80) REVERT: H 172 THR cc_start: 0.8341 (m) cc_final: 0.7968 (p) REVERT: H 178 LEU cc_start: 0.8187 (tp) cc_final: 0.7904 (tt) REVERT: H 215 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7149 (p) REVERT: H 226 VAL cc_start: 0.7909 (t) cc_final: 0.7588 (m) REVERT: H 243 THR cc_start: 0.8695 (m) cc_final: 0.8154 (p) outliers start: 33 outliers final: 24 residues processed: 275 average time/residue: 0.2168 time to fit residues: 82.6220 Evaluate side-chains 291 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 0.0050 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN H 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9022 Z= 0.164 Angle : 0.549 7.501 12238 Z= 0.281 Chirality : 0.042 0.135 1410 Planarity : 0.004 0.044 1537 Dihedral : 4.706 25.961 1235 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.39 % Allowed : 19.07 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1127 helix: 1.84 (0.26), residues: 417 sheet: -0.38 (0.29), residues: 297 loop : -0.12 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS A 213 PHE 0.017 0.001 PHE H 68 TYR 0.023 0.001 TYR D 179 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 1.001 Fit side-chains REVERT: A 29 LYS cc_start: 0.7129 (ttpt) cc_final: 0.6725 (ttpt) REVERT: A 33 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6443 (mt-10) REVERT: A 197 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7789 (ttmm) REVERT: A 210 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7625 (mmtt) REVERT: A 251 ASP cc_start: 0.7255 (t0) cc_final: 0.6993 (t0) REVERT: A 261 ASP cc_start: 0.7008 (t0) cc_final: 0.6741 (t0) REVERT: A 309 ASP cc_start: 0.6430 (m-30) cc_final: 0.6073 (m-30) REVERT: A 330 LYS cc_start: 0.7329 (mmtt) cc_final: 0.6856 (mmtt) REVERT: A 333 GLN cc_start: 0.7457 (tp40) cc_final: 0.6942 (tp-100) REVERT: B 129 ARG cc_start: 0.6519 (mmp80) cc_final: 0.6209 (mmp80) REVERT: B 135 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8122 (m) REVERT: B 168 LEU cc_start: 0.7663 (tp) cc_final: 0.7258 (tp) REVERT: B 189 SER cc_start: 0.8428 (p) cc_final: 0.8112 (p) REVERT: B 205 ASP cc_start: 0.7024 (p0) cc_final: 0.6634 (p0) REVERT: B 219 ARG cc_start: 0.7415 (mmt180) cc_final: 0.7137 (mmt90) REVERT: B 239 ASN cc_start: 0.7377 (m-40) cc_final: 0.7059 (m-40) REVERT: B 251 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7726 (mtt-85) REVERT: B 258 ASP cc_start: 0.7462 (t0) cc_final: 0.6927 (t0) REVERT: B 275 SER cc_start: 0.8110 (t) cc_final: 0.7853 (t) REVERT: B 277 SER cc_start: 0.7979 (t) cc_final: 0.7499 (m) REVERT: B 298 ASP cc_start: 0.7137 (t70) cc_final: 0.6770 (t70) REVERT: B 312 ASP cc_start: 0.5999 (t0) cc_final: 0.5782 (t70) REVERT: B 331 SER cc_start: 0.8165 (OUTLIER) cc_final: 0.7838 (p) REVERT: B 333 ASP cc_start: 0.6186 (m-30) cc_final: 0.5844 (m-30) REVERT: D 98 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8075 (m-40) REVERT: D 154 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8182 (p) REVERT: H 83 MET cc_start: 0.7019 (mmm) cc_final: 0.6793 (tpt) REVERT: H 172 THR cc_start: 0.8296 (m) cc_final: 0.7982 (p) REVERT: H 178 LEU cc_start: 0.8158 (tp) cc_final: 0.7884 (tt) REVERT: H 215 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7118 (p) REVERT: H 243 THR cc_start: 0.8667 (m) cc_final: 0.8152 (p) outliers start: 32 outliers final: 23 residues processed: 268 average time/residue: 0.2143 time to fit residues: 78.6120 Evaluate side-chains 268 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9022 Z= 0.201 Angle : 0.588 15.684 12238 Z= 0.295 Chirality : 0.042 0.178 1410 Planarity : 0.004 0.043 1537 Dihedral : 4.741 27.014 1235 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.28 % Allowed : 20.02 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1127 helix: 1.98 (0.26), residues: 407 sheet: -0.28 (0.29), residues: 289 loop : -0.07 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.004 0.001 HIS A 213 PHE 0.029 0.002 PHE D 218 TYR 0.020 0.001 TYR D 179 ARG 0.006 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.989 Fit side-chains REVERT: A 29 LYS cc_start: 0.7131 (ttpt) cc_final: 0.6751 (ttpt) REVERT: A 33 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6422 (mt-10) REVERT: A 197 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7845 (mtpp) REVERT: A 210 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7447 (mmtt) REVERT: A 251 ASP cc_start: 0.7281 (t0) cc_final: 0.7020 (t0) REVERT: A 261 ASP cc_start: 0.7020 (t0) cc_final: 0.6750 (t0) REVERT: A 309 ASP cc_start: 0.6454 (m-30) cc_final: 0.6145 (m-30) REVERT: A 330 LYS cc_start: 0.7332 (mmtt) cc_final: 0.6852 (mmtt) REVERT: A 333 GLN cc_start: 0.7519 (tp40) cc_final: 0.6984 (tp40) REVERT: B 87 THR cc_start: 0.8385 (m) cc_final: 0.8175 (m) REVERT: B 129 ARG cc_start: 0.6547 (mmp80) cc_final: 0.6208 (mmp80) REVERT: B 135 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8066 (m) REVERT: B 189 SER cc_start: 0.8453 (p) cc_final: 0.8186 (p) REVERT: B 205 ASP cc_start: 0.6967 (p0) cc_final: 0.6763 (p0) REVERT: B 219 ARG cc_start: 0.7445 (mmt180) cc_final: 0.7133 (mmt90) REVERT: B 230 ASN cc_start: 0.7497 (m-40) cc_final: 0.7071 (m-40) REVERT: B 255 LEU cc_start: 0.8055 (mt) cc_final: 0.7839 (mp) REVERT: B 258 ASP cc_start: 0.7441 (t0) cc_final: 0.6875 (t0) REVERT: B 275 SER cc_start: 0.8104 (t) cc_final: 0.7859 (t) REVERT: B 277 SER cc_start: 0.8152 (t) cc_final: 0.7632 (m) REVERT: B 298 ASP cc_start: 0.7132 (t70) cc_final: 0.6765 (t70) REVERT: B 312 ASP cc_start: 0.6044 (t0) cc_final: 0.5825 (t70) REVERT: B 333 ASP cc_start: 0.6182 (m-30) cc_final: 0.5968 (m-30) REVERT: D 154 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8186 (p) REVERT: H 59 TYR cc_start: 0.7373 (m-80) cc_final: 0.7052 (m-10) REVERT: H 67 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7229 (ttp80) REVERT: H 172 THR cc_start: 0.8323 (m) cc_final: 0.7962 (p) REVERT: H 178 LEU cc_start: 0.8181 (tp) cc_final: 0.7913 (tt) REVERT: H 215 THR cc_start: 0.7488 (m) cc_final: 0.7149 (p) outliers start: 31 outliers final: 24 residues processed: 267 average time/residue: 0.2145 time to fit residues: 78.1661 Evaluate side-chains 276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.0170 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9022 Z= 0.187 Angle : 0.570 11.158 12238 Z= 0.290 Chirality : 0.042 0.172 1410 Planarity : 0.004 0.042 1537 Dihedral : 4.688 28.148 1235 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.07 % Allowed : 20.97 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1127 helix: 1.88 (0.26), residues: 415 sheet: -0.35 (0.29), residues: 298 loop : -0.02 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 111 HIS 0.004 0.001 HIS A 213 PHE 0.033 0.002 PHE D 218 TYR 0.022 0.001 TYR D 179 ARG 0.009 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.954 Fit side-chains REVERT: A 29 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6688 (ttpt) REVERT: A 33 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6418 (mt-10) REVERT: A 197 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7818 (mtpp) REVERT: A 251 ASP cc_start: 0.7278 (t0) cc_final: 0.7020 (t0) REVERT: A 261 ASP cc_start: 0.6986 (t0) cc_final: 0.6728 (t0) REVERT: A 309 ASP cc_start: 0.6391 (m-30) cc_final: 0.6126 (m-30) REVERT: A 330 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6861 (mmtt) REVERT: A 333 GLN cc_start: 0.7544 (tp40) cc_final: 0.6850 (tp40) REVERT: B 87 THR cc_start: 0.8305 (m) cc_final: 0.8031 (m) REVERT: B 129 ARG cc_start: 0.6549 (mmp80) cc_final: 0.6217 (mmp80) REVERT: B 132 ASN cc_start: 0.8306 (p0) cc_final: 0.8072 (p0) REVERT: B 135 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8149 (m) REVERT: B 168 LEU cc_start: 0.7437 (tt) cc_final: 0.7122 (tp) REVERT: B 219 ARG cc_start: 0.7380 (mmt180) cc_final: 0.7090 (mmt90) REVERT: B 232 ILE cc_start: 0.8510 (tt) cc_final: 0.8170 (tt) REVERT: B 239 ASN cc_start: 0.7356 (m-40) cc_final: 0.7063 (m-40) REVERT: B 258 ASP cc_start: 0.7442 (t0) cc_final: 0.6868 (t0) REVERT: B 275 SER cc_start: 0.8099 (t) cc_final: 0.7857 (t) REVERT: B 277 SER cc_start: 0.8148 (t) cc_final: 0.7644 (m) REVERT: B 298 ASP cc_start: 0.7043 (t70) cc_final: 0.6725 (t70) REVERT: B 312 ASP cc_start: 0.6011 (t0) cc_final: 0.5798 (t70) REVERT: B 333 ASP cc_start: 0.6140 (m-30) cc_final: 0.5872 (m-30) REVERT: D 121 MET cc_start: 0.6541 (mtm) cc_final: 0.6315 (mmm) REVERT: D 154 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8161 (p) REVERT: D 162 ILE cc_start: 0.7393 (mt) cc_final: 0.7137 (tt) REVERT: H 59 TYR cc_start: 0.7319 (m-80) cc_final: 0.6982 (m-10) REVERT: H 67 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7354 (ttp80) REVERT: H 97 VAL cc_start: 0.8215 (t) cc_final: 0.8008 (t) REVERT: H 172 THR cc_start: 0.8271 (m) cc_final: 0.7952 (p) REVERT: H 178 LEU cc_start: 0.8127 (tp) cc_final: 0.7914 (tt) REVERT: H 226 VAL cc_start: 0.7863 (t) cc_final: 0.7505 (m) outliers start: 29 outliers final: 24 residues processed: 255 average time/residue: 0.2007 time to fit residues: 71.6736 Evaluate side-chains 269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.0470 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9022 Z= 0.279 Angle : 0.595 7.964 12238 Z= 0.304 Chirality : 0.045 0.307 1410 Planarity : 0.004 0.042 1537 Dihedral : 4.838 28.543 1235 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.71 % Allowed : 20.44 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1127 helix: 1.95 (0.26), residues: 400 sheet: -0.29 (0.29), residues: 295 loop : -0.22 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 111 HIS 0.005 0.001 HIS A 213 PHE 0.039 0.002 PHE A 336 TYR 0.022 0.002 TYR D 179 ARG 0.014 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.875 Fit side-chains REVERT: A 29 LYS cc_start: 0.7120 (ttpt) cc_final: 0.6765 (ttpt) REVERT: A 33 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6452 (mt-10) REVERT: A 197 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7837 (mtpp) REVERT: A 251 ASP cc_start: 0.7348 (t0) cc_final: 0.7101 (t0) REVERT: A 261 ASP cc_start: 0.7037 (t0) cc_final: 0.6764 (t0) REVERT: A 309 ASP cc_start: 0.6417 (m-30) cc_final: 0.6164 (m-30) REVERT: A 330 LYS cc_start: 0.7358 (mmtt) cc_final: 0.6967 (mmtt) REVERT: B 87 THR cc_start: 0.8280 (m) cc_final: 0.8023 (m) REVERT: B 129 ARG cc_start: 0.6576 (mmp80) cc_final: 0.6290 (mmp80) REVERT: B 135 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8251 (m) REVERT: B 177 THR cc_start: 0.8203 (t) cc_final: 0.7977 (p) REVERT: B 205 ASP cc_start: 0.7047 (p0) cc_final: 0.6696 (p0) REVERT: B 219 ARG cc_start: 0.7479 (mmt180) cc_final: 0.7227 (mmt90) REVERT: B 239 ASN cc_start: 0.7368 (m-40) cc_final: 0.6974 (m-40) REVERT: B 258 ASP cc_start: 0.7448 (t0) cc_final: 0.6860 (t0) REVERT: B 275 SER cc_start: 0.8132 (t) cc_final: 0.7922 (t) REVERT: B 277 SER cc_start: 0.8156 (t) cc_final: 0.7638 (m) REVERT: B 298 ASP cc_start: 0.7127 (t70) cc_final: 0.6773 (t70) REVERT: B 312 ASP cc_start: 0.6096 (t0) cc_final: 0.5861 (t70) REVERT: D 102 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7907 (t0) REVERT: D 121 MET cc_start: 0.6565 (mtm) cc_final: 0.6354 (mmm) REVERT: D 154 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8115 (p) REVERT: D 162 ILE cc_start: 0.7542 (mt) cc_final: 0.7285 (tt) REVERT: H 59 TYR cc_start: 0.7373 (m-80) cc_final: 0.7054 (m-80) REVERT: H 67 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7330 (ttp80) REVERT: H 97 VAL cc_start: 0.8243 (t) cc_final: 0.8026 (t) REVERT: H 172 THR cc_start: 0.8309 (m) cc_final: 0.7971 (p) REVERT: H 178 LEU cc_start: 0.8172 (tp) cc_final: 0.7917 (tt) REVERT: H 184 SER cc_start: 0.8222 (p) cc_final: 0.7912 (m) outliers start: 35 outliers final: 30 residues processed: 260 average time/residue: 0.1958 time to fit residues: 71.9479 Evaluate side-chains 274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 0.0070 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9022 Z= 0.188 Angle : 0.582 9.091 12238 Z= 0.296 Chirality : 0.044 0.237 1410 Planarity : 0.004 0.042 1537 Dihedral : 4.808 30.036 1235 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.97 % Allowed : 21.72 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1127 helix: 2.01 (0.26), residues: 400 sheet: -0.30 (0.30), residues: 294 loop : -0.20 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 111 HIS 0.004 0.001 HIS A 213 PHE 0.033 0.002 PHE A 336 TYR 0.020 0.001 TYR D 179 ARG 0.013 0.001 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 1.021 Fit side-chains REVERT: A 29 LYS cc_start: 0.7099 (ttpt) cc_final: 0.6717 (ttpt) REVERT: A 33 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6421 (mt-10) REVERT: A 197 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7777 (mtpp) REVERT: A 251 ASP cc_start: 0.7330 (t0) cc_final: 0.7077 (t0) REVERT: A 261 ASP cc_start: 0.7005 (t0) cc_final: 0.6722 (t0) REVERT: A 309 ASP cc_start: 0.6383 (m-30) cc_final: 0.6181 (m-30) REVERT: A 330 LYS cc_start: 0.7358 (mmtt) cc_final: 0.6964 (mmtt) REVERT: B 87 THR cc_start: 0.8290 (m) cc_final: 0.8045 (m) REVERT: B 129 ARG cc_start: 0.6546 (mmp80) cc_final: 0.6253 (mmp80) REVERT: B 132 ASN cc_start: 0.8352 (p0) cc_final: 0.8109 (p0) REVERT: B 135 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8152 (m) REVERT: B 188 MET cc_start: 0.7600 (mmm) cc_final: 0.7195 (mmm) REVERT: B 189 SER cc_start: 0.8395 (p) cc_final: 0.8192 (p) REVERT: B 205 ASP cc_start: 0.7064 (p0) cc_final: 0.6736 (p0) REVERT: B 219 ARG cc_start: 0.7476 (mmt180) cc_final: 0.7241 (mmt90) REVERT: B 239 ASN cc_start: 0.7312 (m-40) cc_final: 0.6776 (m-40) REVERT: B 256 ARG cc_start: 0.7979 (mpp80) cc_final: 0.7508 (mtm180) REVERT: B 258 ASP cc_start: 0.7391 (t0) cc_final: 0.6762 (t0) REVERT: B 275 SER cc_start: 0.8128 (t) cc_final: 0.7861 (t) REVERT: B 277 SER cc_start: 0.8171 (t) cc_final: 0.7731 (m) REVERT: B 298 ASP cc_start: 0.7182 (t70) cc_final: 0.6802 (t70) REVERT: B 312 ASP cc_start: 0.5959 (t0) cc_final: 0.5759 (t70) REVERT: D 121 MET cc_start: 0.6579 (mtm) cc_final: 0.6361 (mmm) REVERT: D 154 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8084 (p) REVERT: D 162 ILE cc_start: 0.7437 (mt) cc_final: 0.7171 (tt) REVERT: H 59 TYR cc_start: 0.7339 (m-80) cc_final: 0.7019 (m-10) REVERT: H 67 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7376 (ttp80) REVERT: H 97 VAL cc_start: 0.8215 (t) cc_final: 0.8007 (t) REVERT: H 172 THR cc_start: 0.8265 (m) cc_final: 0.7943 (p) REVERT: H 178 LEU cc_start: 0.8133 (tp) cc_final: 0.7889 (tt) REVERT: H 184 SER cc_start: 0.8207 (p) cc_final: 0.7899 (m) outliers start: 28 outliers final: 25 residues processed: 256 average time/residue: 0.1922 time to fit residues: 69.5208 Evaluate side-chains 269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 88 ASN D 131 ASN D 194 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124391 restraints weight = 12530.426| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.04 r_work: 0.3448 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9022 Z= 0.171 Angle : 0.577 8.887 12238 Z= 0.291 Chirality : 0.043 0.208 1410 Planarity : 0.004 0.042 1537 Dihedral : 4.727 31.029 1235 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.86 % Allowed : 22.03 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1127 helix: 2.04 (0.26), residues: 406 sheet: -0.19 (0.30), residues: 288 loop : -0.32 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS A 213 PHE 0.030 0.002 PHE A 336 TYR 0.019 0.001 TYR D 179 ARG 0.011 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.66 seconds wall clock time: 45 minutes 48.75 seconds (2748.75 seconds total)